[Mrtrix-discussion] nifti format

Tue Jul 12 05:04:03 PDT 2011

Hello Donald

Thank for your quick response. I totally agree about the recipe of 
chaos. The nifti definition was a very important initiative to add the 
orientation in the header
(the analyze format was just a shame) but The 2 matrix make it crazy. So 
a reasonable solution is to make both matrix identical.

For the last point I am still not convince about the necessity to change 
the header (and the data accordingly). As you said both file are 
coherent and are display exactly the same
in mrview (and also in SPM software). But it is not the case for viewer 
that display the data matrix (with a bad handling of the orientation matrix)
For instance with trackvis, the change from mrtrix make it to swap left 
and right ...

Since you seems to handle the orientation properly, why not to keep the 
hdr unchanged (for both matrix by the way) ? This will facilitate
interoperability between software.

Since I am beggining to become a new fan of mrtrix, I think I can 
mannage it like it is ... but it seems to me it will though be an 
improvement ...

Thanks

Romain

Donald Tournier wrote:
> Salut Romain, 
>
>     I have some question nifti file produce by mrtrix
>
>     _depending on the data type I can not see file in other nifti
>     viewer (fslview or spm)
>     for instance (  Data type:         bitwise)
>
>
> Yes, bitwise data are rarely supported by other packages, which is a 
> shame since it is in the NIfTI standard.
>  
>
>     I guess I can test different output type with mrconvert but I
>     can't find on the docs
>     which string to give to the  -datatype option
>
>
> Yes, that's the best way to deal with the issue. The list of data 
> types is in the docs, but maybe not the most obvious place:
> http://www.brain.org.au/software/mrtrix/general/formats.html#datatypes
>  
>
>     _A second point is about the 2 orientation matrix from the nifti
>     header
>     The sform is correct, but the qform just set an identity
>     orientation (with the voxel size)
>     why not to set both orientation to the same value ?
>     I am not sure if it is specify in the nifti definition which
>     orientation to use first, but I would set both orientation
>     identical ...
>
>
> Yes, you're right, the NIfTI standard does specifies that both qform 
> and sform can coexist: apparently you can use whichever you like 
> depending on your specific application context. MRtrix will always use 
> the sform if it's available, otherwise the qform is used. I personally 
> find having two different transforms in the same file confusing, 
> sounds like a recipe for chaos to me... 
>
> In any case, you're right that there is no reason why the same 
> transforms can't both be stored in the header. I might make that 
> change for the next release.
>  
>
>     _A last point: I have notice that when nifti file are created
>     (based on other nifti file) there is a change of the nifti
>     orientation in the header :
>     I have orientation with negative pixel size but ater mrconvert it
>     will be change with positive valu
>     for instance with a sform
>     -1.71875 0 0 110 0 1.39752 -1.16425 -33.0028 -1.71875e-16 1.00052
>     1.6262 -140.284 0 0 0 1
>     but file produce by mrconvert will then have always positive voxel
>     size
>     1.71875 0 0  -108.281 -0 1.39752  -1.16425 -33.0028 1.71875e-16
>     1.00052 1.6262 -140.284 0 0 0 1
>
>     Why not to keep the original nifti header orientation (with both
>     sform and qform set) ... ?
>     I do not realy understand why this change and I wonder if this
>     imply a reordening of the data matrix
>
>
> Yes, this can happen. This is due to the fact that after loading the 
> image header, MRtrix will modify the transform if it's not near-axial. 
> This is to ensure that the x-axis is always as close to left-right as 
> possible, the y-axis is as close to posterior-anterior as possible, 
> etc. This also means that the strides used to navigate around the data 
> get changed accordingly - in your case, the x-axis would simply have 
> been inverted. You'll also notice that the translation x coordinate 
> has changed from 110 to -108.281, since after inverting the x-axis the 
> 'origin' will now be in the opposite corner. The data will also have 
> been reordered in the output file for that reason, but will (or at 
> least should) always remain consistent with the header. The check is 
> to display both files in MRView, they should align perfectly. 
>
> Someone else had a related issue displaying a non-axial NIfTI image in 
> FSLView, and they trying to overlay another NIfTI image generated with 
> MRtrix from the same image. The problem was also related to the fact 
> that MRtrix will change the transform for non-axial images, and 
> FSLView will not account for that. More info in this thread:
>  http://www.nitrc.org/pipermail/mrtrix-discussion/2009-April/000065.html
>
>
> Cheers,
>
> Donald.
>
>
>     Many thanks
>
>     Romain
>
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>
>
>
> -- 
> Jacques-Donald Tournier (PhD)
> Brain Research Institute, Melbourne, Australia
> Tel: +61 (0)3 9035 7033